10-100372754-C-T

Variant names:

• chr10-100372754-C-T
• rs569184
• ENST00000693438.3:n.1015G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693438.3(ENSG00000289301):​n.1015G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,016 control chromosomes in the GnomAD database, including 4,153 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.19 (4153 hom., cov: 32)
• Consequence: ENSG00000289301 ENST00000693438.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 4 publications found

Genes affected

ENSG00000289301 (HGNC:):

OLMALINC (HGNC:28060): (oligodendrocyte maturation-associated long intergenic non-coding RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693438.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289301	ENST00000693438.3		n.1015G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289301	ENST00000769404.1		n.343+246G>A		intron	N/A
	ENSG00000289301	ENST00000769405.1		n.395+246G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29275 AN: 151898 Hom.: 4140 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.193 AC: 29320 AN: 152016 Hom.: 4153 Cov.: 32 AF XY: 0.192 AC XY: 14266 AN XY: 74302

African (AFR) AF: 0.397 AC: 16431 AN: 41398

American (AMR) AF: 0.119 AC: 1814 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1132 AN: 5168

South Asian (SAS) AF: 0.190 AC: 916 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1436 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0994 AC: 6757 AN: 67990

Other (OTH) AF: 0.157 AC: 332 AN: 2110

Alfa AF: 0.119 Hom.: 638

Bravo AF: 0.199

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.74
DANN	Benign	0.53
PhyloP100		-0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs569184; hg19: chr10-102132511;